Friday, April 1, 2011

GREAT: Genomic Regions Enrichment of Annotations Tool

great (Bejerano Lab, Stanford University)
GREAT Input: Genomic Regions Enrichment of Annotations Tool, Bejerano Lab, Stanford University: GREAT predicts functions of cis-regulatory regions.
Many coding genes are well annotated with their biological functions. Non-coding regions typically lack such annotation. GREAT assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes. Thus, it is particularly useful in studying cis functions of sets of non-coding genomic regions. Cis-regulatory regions can be identified via both experimental methods (e.g. chromatin immunoprecipitation followed by massively parallel sequencing) and by computational methods (e.g. sequence conservation in a given clade).